[2024-01-24 12:57:48,998] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:48,999] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:48,999] [INFO] DQC Reference Directory: /var/lib/cwl/stg612f239a-690e-4bac-9bc6-bae073901d68/dqc_reference
[2024-01-24 12:57:50,197] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:50,198] [INFO] Task started: Prodigal
[2024-01-24 12:57:50,198] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c154d35-8385-4e13-81af-b90d6d32ccce/GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/cds.fna -a GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:58:07,013] [INFO] Task succeeded: Prodigal
[2024-01-24 12:58:07,013] [INFO] Task started: HMMsearch
[2024-01-24 12:58:07,013] [INFO] Running command: hmmsearch --tblout GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg612f239a-690e-4bac-9bc6-bae073901d68/dqc_reference/reference_markers.hmm GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:58:07,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:58:07,260] [INFO] Found 6/6 markers.
[2024-01-24 12:58:07,303] [INFO] Query marker FASTA was written to GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 12:58:07,303] [INFO] Task started: Blastn
[2024-01-24 12:58:07,304] [INFO] Running command: blastn -query GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg612f239a-690e-4bac-9bc6-bae073901d68/dqc_reference/reference_markers.fasta -out GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:08,031] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:08,035] [INFO] Selected 21 target genomes.
[2024-01-24 12:58:08,035] [INFO] Target genome list was writen to GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 12:58:08,042] [INFO] Task started: fastANI
[2024-01-24 12:58:08,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c154d35-8385-4e13-81af-b90d6d32ccce/GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna.gz --refList GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:58:24,702] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:24,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg612f239a-690e-4bac-9bc6-bae073901d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:58:24,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg612f239a-690e-4bac-9bc6-bae073901d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:58:24,718] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:58:24,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:58:24,718] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	100.0	1730	1733	95	conclusive
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	87.9403	1259	1733	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.4664	621	1733	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	79.4262	617	1733	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	79.3822	724	1733	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	79.0389	531	1733	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.0228	611	1733	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.7283	597	1733	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	78.7157	528	1733	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.5621	619	1733	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	78.2686	491	1733	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	78.2505	494	1733	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	78.0071	354	1733	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	77.9346	359	1733	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.7525	316	1733	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.6273	308	1733	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.5453	314	1733	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.4986	391	1733	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.4762	298	1733	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.1089	333	1733	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.9534	279	1733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:58:24,720] [INFO] DFAST Taxonomy check result was written to GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 12:58:24,721] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:58:24,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:58:24,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg612f239a-690e-4bac-9bc6-bae073901d68/dqc_reference/checkm_data
[2024-01-24 12:58:24,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:58:24,769] [INFO] Task started: CheckM
[2024-01-24 12:58:24,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/checkm_input GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 12:59:16,191] [INFO] Task succeeded: CheckM
[2024-01-24 12:59:16,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:59:16,209] [INFO] ===== Completeness check finished =====
[2024-01-24 12:59:16,209] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:59:16,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 12:59:16,210] [INFO] Task started: Blastn
[2024-01-24 12:59:16,210] [INFO] Running command: blastn -query GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg612f239a-690e-4bac-9bc6-bae073901d68/dqc_reference/reference_markers_gtdb.fasta -out GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:59:17,319] [INFO] Task succeeded: Blastn
[2024-01-24 12:59:17,322] [INFO] Selected 12 target genomes.
[2024-01-24 12:59:17,322] [INFO] Target genome list was writen to GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:59:17,373] [INFO] Task started: fastANI
[2024-01-24 12:59:17,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c154d35-8385-4e13-81af-b90d6d32ccce/GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna.gz --refList GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:59:29,501] [INFO] Task succeeded: fastANI
[2024-01-24 12:59:29,511] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:59:29,511] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900302455.1	s__Ruegeria_E mediterranea	100.0	1730	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	99.84	99.84	0.96	0.96	2	conclusive
GCF_017743935.1	s__Ruegeria_E sp017743935	91.1654	1483	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	87.9207	1261	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900537075.1	s__Ruegeria_E sp900537075	84.4661	1219	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	79.4584	622	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031355.1	s__Ruegeria arenilitoris_C	79.2164	624	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
GCF_013032025.1	s__Ruegeria atlantica_C	78.9372	530	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCA_014872875.1	s__WKFI01 sp014872875	78.8799	557	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	78.7221	597	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032005.1	s__Ruegeria atlantica_A	78.6986	551	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.11	97.00	0.94	0.90	12	-
GCF_013033515.1	s__Ruegeria sp013033515	78.6251	507	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.60	97.60	0.95	0.93	6	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	77.6654	274	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:59:29,513] [INFO] GTDB search result was written to GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 12:59:29,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:59:29,517] [INFO] DFAST_QC result json was written to GCF_900302455.1_T.mediterraneusCECT7615_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 12:59:29,517] [INFO] DFAST_QC completed!
[2024-01-24 12:59:29,517] [INFO] Total running time: 0h1m41s